This invention relates to biomolecular arrays and, particularly, to methods and apparatus for depositing biological materials in a pattern of array features on a surface of a solid support.
Arrays of binding agents have become an increasingly important tool in the biotechnology industry and related fields. Such arrays, in which such binding agents as oligonucleotides or peptides are deposited onto a solid support surface in the form of an array or pattern, can be useful in a variety of applications, including gene expression analysis, drug screening, nucleic acid sequencing, mutation analysis, and the like.
Such arrays may be prepared in any of a variety of different ways. For example, DNA arrays may be prepared manually by spotting DNA onto the surface of a substrate with a micro pipette. See, Khrapko et al. (1991), DNA Sequence 1:375-388. Or, a dot-blot approach or a slot-blot approach may be employed in which a vacuum manifold transfers aqueous DNA samples from a plurality of wells to a substrate surface. Or, an array of pins can be dipped into an array of fluid samples and then contacted with the substrate surface to produce the array of sample materials. Or, an array of capillaries can be used to produce biopolymeric arrays, as described for example in International Patent Publication WO 95/35505.
In an alternative approach, arrays of biopolymeric agents are constructed in discrete regions on the surface of the substrate. See, e.g., U.S. Pat. No. 5,143,854; and Fodor, et al. (1991), Science 251:767-773.
There is a continued interest in developing methods and devices for making arrays of biomolecules, in which the apparatus is less complicated and more automated and the methods reduce waste of biological material that may be in limited supply, and which result in efficient and reproducible rapid production of more versatile and reliable arrays.
Arrays of biomolecular materials, and methods for their fabrication, are described for example in U.S. Pat. Nos.: 5,242,974; 5,384,261; 5,405,783; 5,412,087; 5,424,186; 5,429,807; 5,436,327; 5,445,934; 5,472,672; 5,527,681; 5,529,756; 5,545,531; 5,554,501; 5,556,752; 5,561,071; 5,599,695; 5,624,711; 5,639,603; and 5,658,734; in International Patent Publications WO 93/17126; WO 95/11995; and WO 95/35505; and in European Patent Publications EP 742 287; and EP 799 897.
Other publications of interest include: Lockhart, et al. (1996), Nature Biotechnology 14: 1675-1680; Schena, et al. (1995), Science 270: 467-470; Schena, et al. (1996), Proc. Nat""l. Acad. Sci. USA 93:10614-10619; Shalon, et al. (1996), Genome Res. 6: 639-645; Milosavljevic, et al. (1996), Genome Res. 6:132-141; Nguyen, et al. (1995), Genomics 29: 207-216; Pixc3xa9tu, et al. (1996), Genome Res. 6: 492-503; Zhao, et al. (1995), Gene 166:207-213; Chalifour, et al. (1994), Anal. Biochem. 216:299-304; Heller, et al. (1997), Proc. Nat""l Acad. Sci. USA 94: 2150-2155; Lehrach, et al. (1990), Hybridization Fingerprinting in Genome Mapping and Sequencing, Genome Analysis, Vol. 1 (Davies and Tilgham, eds.) (Cold Spring Harbor Press) pp. 39-81; and Schema (1996), BioAssays 18: 427-431.
The use of inkjet printing devices to dispense biochemical agents such as proteins and nucleic acids is suggested or disclosed in, for example, U.S. Pat. Nos. 5,658,802; 5,338,688; 5,700,637; 5,474,796; 4,877,745; and 5,449,754.
In one general aspect the invention features apparatus for delivering a plurality of different biological materials onto discrete locations on a receiving surface, the apparatus including a plurality of orifices in an orifice member, at least six delivery chambers each in fluid conducting relationship with at least one of the orifices, a plurality of reservoirs each in fluid communication with at least one of the delivery chambers, and means associated with each orifice for propelling fluid through the associated orifice from the delivery chamber that is in fluid conducting relationship with the orifice.
In another general aspect the invention features apparatus for delivering a plurality of different biological materials onto discrete locations on a receiving surface, the apparatus including a plurality of orifices in an orifice member, at least six delivery chambers each in fluid conducting relationship with at least one of the orifices, a plurality of reservoirs each in fluid communication with at least one of the delivery chambers, means associated with each orifice for propelling fluid through the associated orifice from the delivery chamber that is in fluid conducting relationship with the orifice, and a vent for commonly venting at least two of the reservoirs.
In some embodiments the propelling means propels the fluid through the associated orifice by forming a bubble that displaces the fluid; particular bubble-forming means include a source of heat such as an electrical resistor. In other embodiments the propelling means propels the fluid through the associated orifice by electromechanical displacement; particular electromechanical displacement means include a piezoelectric device.
In some embodiments the orifice member is a generally planar orifice plate, and the orifices provide openings through from an inner surface to an exit surface of the plate; the apparatus further includes a back member having a generally planar surface facing the inner surface of the orifice plate; and the inner surface of the orifice plate and the facing surface of the back member are spaced apart by a barrier. The barrier is configured so that the barrier, the inner surface of the orifice plate, and the facing surface of the back member define the delivery chambers. In some such embodiments the fluid propelling means are situated on or in the back member, or on or in the barrier. Usually, the back member is constructed as a silicon die, and the fluid propelling means are formed within the silicon die by techniques that are conventional to solid state electronic device construction.
In another general embodiment the invention features apparatus for depositing a plurality of different biological materials onto discrete locations on a receiving surface, the apparatus including an orifice plate defining a plurality of orifices; a substrate connected to the orifice plate and defining a plurality of delivery chambers and a plurality of reservoirs, each of the orifices being in fluid communication with a reservoir by way of a delivery chamber; means adjacent each orifice for propelling fluid through the orifice from the delivery chamber that provides fluid communication with the orifice and reservoir; and common means for generating a pressure differential within at least a plurality of the delivery chambers.
In some embodiments each delivery chamber is connected to a fluid reservoir by way of a conduit. Accordingly, in another general aspect the invention features apparatus for depositing a plurality of different biological materials onto discrete locations on a receiving surface, the apparatus comprising an orifice member defining a plurality of orifices therethrough from a first surface to a second surface thereof; a barrier affixed to the first surface of the orifice member, the barrier and the orifice member together defining a plurality of delivery chambers each of which is in fluid communication with one of the orifices, and the barrier and the orifice member together defining a plurality of fluid reservoirs; the orifice member further having a plurality of channels, each of which has an opening in the first surface to one of the delivery chambers and an opening in the first surface to one of the reservoirs, and each of which provides fluid communication between the delivery chamber and the fluid reservoir to which it opens; and means associated with each orifice for propelling fluid through the orifice from the delivery chamber that is in fluid communication with the orifice.
The apparatus according to the invention is usefull in methods for delivering biological materials in a patterned array on a solid surface.
Accordingly, in another general aspect the invention features a method for delivering a plurality of different biological materials onto discrete locations on a receiving surface, the method comprising loading a fluid medium containing one of the different biological materials into one of the delivery chambers of the apparatus, each propelling means when activated propelling a quantity of said fluid medium along a delivery path away from the associated orifice member; positioning the apparatus in relation to the receiving surface so that the orifice member is proximate the receiving surface and the delivery path for at least one selected fluid medium intersects the receiving surface at a locus of intersection; moving the apparatus in relation to the receiving surface so that the locus of intersection moves on the receiving surface; activating the propelling means associated with the orifice when the locus of intersection is at a first location on the surface onto which delivery of the selected fluid medium is desired; and repeating the moving and activating steps to deliver the plurality of different biological materials onto discrete locations on the surface.
In another general aspect the invention features a biomolecular array made using the apparatus of the invention or according to the method.
In another configuration, the invention features apparatus for delivering a plurality of different biological materials onto discrete locations on a surface, the apparatus comprising a generally planar substrate having a thickness and a contoured first surface and an edge, and a generally planar cover affixed to the first surface, the contoured first surface and the cover together defining a plurality of enclosed delivery chambers, a plurality of orifices on the edge, and a channel providing fluid communication between each chamber and at least one of the orifices; and common means for generating a pressure differential within at least two of the delivery chambers.
The apparatus of the invention is readily adaptable for automated handling of large numbers of different materials to make arrays of small dimensions and having a large number of array features.
Accordingly, in another general aspect the invention features a method for loading a plurality of different fluids into printing apparatus having a plurality of orifices in an orifice member, a plurality of delivery chambers each in fluid conducting relationship with at least one of the orifices, and means associated with each orifice for propelling fluid through the associated orifice from the delivery chamber that is in fluid conducting relationship with the orifice, and a vent for common venting at least two of the delivery chambers, the method comprising contacting the orifices with a fluid outside the delivery chamber and permitting the outside fluid to flow through the orifices into the delivery chambers. In some embodiments means for reducing pressure in the reservoirs is included, and can be operated to assist the flow of the fluid.
Preferably, where the apparatus is employed for construction of arrays having small dimensions and a high number of discrete array features in high density, the apparatus is part of a device that provides for suitable positioning of the deposition apparatus in relation to the receiving surface of the array substrate; for movement of the deposition apparatus in relation to the receiving surface as, for example, by scanning; and for activation of the propelling means at appropriate times during scanning or at appropriate locations to deposit the selected materials at the desired sites on the receiving surface. Portions or all of these functions can be automated and placed under microprocessor control employing suitable computer programs and user interface.
Other aspects and advantages of the invention will be apparent from the following detailed description, taken in conjunction with the accompanying drawings, illustrating by way of example the principles of the invention.